1Release Note 2 3After v3.2.7 (not yet released) 4 * Move to semantic versioning scheme (see https://semver.org/). 5 Release numbers are MAJOR.MINOR.PATCH where a new MAJOR release 6 number means backward incompatible changes were made, a new MINOR 7 number means backward compatible features were added, and a new 8 PATCH number means backward compatible bugfixes were made. We may 9 or may not use transient suffixes like "-alpha", "-beta" and "-rcN" 10 as well at times. 11 12v3.2.7 (Feb 13 2019) 13 * Added lognormal and flat ordered dirichelet distributions as 14 alternatives to the gamma prior on site variation across sites. 15 * Added new, optional moves for the fossilized birth-death model. 16 * Added new, optional parsimony-guided moves for non-clock trees. 17 * Support for Beagle 3 added. 18 * Added support for FMA and AVX instructions in built-in likelihood 19 calculators for 4by4 nucleotide models. 20 * Added basic command line option support on Unix systems (-h,-i,-v) 21 * Various minor bug fixes. 22 23v3.2.6 (Nov 25 2015) 24 * Add invertebrate mt, Echinoderm and Euplotid codes [lset code=invermt]. 25 * Fix a bug of updating brls in tree-stretch move. 26 * Correct the proposal ratio in the add/delete branch move. 27 * Add more coding options for restriction site chars. 28 29v3.2.5 (Apr 8 2015) 30 * Fix pdf in the coalescent prior. 31 * Fix a few issues when appending to the previous run. 32 * Improve the efficiency of moving ancestral fossils. 33 * Add lognormal rate variation among sites [lset rate=lnorm]. 34 * Add parsimony-biased SPR and TBR proposals (for developers). 35 * Other minor bug fixes and improvements. 36 37v3.2.4 (Jan 27 2015) 38 * Correct the proposal ratio in the node slider move for non-clock tree. 39 * Fix reporting ancestral states under GTR+I+G model. 40 * Fix the sliding window in the move of updating omega in codon model. 41 * Fix the likelihood and proposal ratio of NaN in the multi-species 42 coalescent analysis. 43 * Correct screen output messages for a few commands. 44 * Fix the interaction of MrBayes with Beagle for the Windows executable. 45 * Fix prior pdf of relative rates (rate multipliers). 46 47v3.2.3 (Oct 22 2014) 48 * Correct the proposal ratio in the extending TBR move for non-clock tree. 49 * Fix numerical error of calculating proposal ratio in 50 parsimony-biased SPR moves. 51 * Set unconstrained:gammadir prior as default to help avoid 52 overestimating branch lengths. 53 * Add clock:fossilization prior for total-evidence dating analysis. 54 * Add LG model to Aamodelpr [prset aamodelpr=fixed(LG)]. 55 * Rearrange the code to be more concise. 56 * Other minor bug fixes and improvements. 57 58v3.2.2 (Aug 22 2013) 59 * Disable LIKE_EPSILON warning for standard users. 60 * Fix segmentation fault errors in 64bit version. 61 * Fix some issues when dealing with constraints. 62 * Fix setting aarevmatpr parameters to fixed for GTR. 63 * Other bug fixes and improvements. 64 65v3.2.1 (Feb 8 2012) 66v3.2.0 (Nov 16 2011) 67 Major release. 68